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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ), 'gf_id' => 'HOM05D001192', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001192' ), 'data_identifier' => 'HOM05D001192', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001192', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '93' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10310' => 'bna', 'A02p22010' => 'bna', 'A02p29730' => 'bna', 'A06p46120' => 'bna', 'A07p14640' => 'bna', 'A07p43350' => 'bna', 'A07p43410' => 'bna', 'A08p28580' => 'bna', 'A09p36340' => 'bna', 'A09p42560' => 'bna', 'Aa31LG4G8150' => 'aar', 'Aa31LG6G1090' => 'aar', 'Aa31LG6G5530' => 'aar', 'Aa31LG7G6160' => 'aar', 'Aa31LG9G6740' => 'aar', 'Actinidia10313' => 'ach', 'Actinidia30760' => 'ach', 'Actinidia32341' => 'ach', 'Actinidia33714' => 'ach', 'Actinidia39587' => 'ach', 'Actinidia39588' => 'ach', 'Ah.09g232490' => 'amhyb', 'Ah.09g232500' => 'amhyb', 'AL1G35670' => 'aly', 'AL1G44100' => 'aly', 'AL2G38410' => 'aly', 'AL7G35980' => 'aly', 'AL8G12300' => 'aly', 'Aqoxy1G01678' => 'aox', 'Aqoxy4G00067' => 'aox', 'Aqoxy6G00596' => 'aox', 'arahy.Tifrunner.gnm1.ann1.K4VSH4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQL2JJ' => 'arhy', 'AT1G22220' => 'ath', 'AT1G30200' => 'ath', 'AT1G78100' => 'ath', 'AT4G18380' => 'ath', 'AT5G46170' => 'ath', 'ATR0307G014' => 'atr', 'ATR0564G166' => 'atr', 'ATR0787G224' => 'atr', 'ATR1098G127' => 'atr', 'Atru.chr10.1166' => 'acertr', 'Atru.chr13.1218' => 'acertr', 'Atru.chr13.1224' => 'acertr', 'Atru.chr3.2805' => 'acertr', 'AUR62000176' => 'cqu', 'AUR62002696' => 'cqu', 'AUR62030153' => 'cqu', 'AUR62039834' => 'cqu', 'BcaB03g11899' => 'bca', 'BcaB03g14225' => 'bca', 'BcaB03g15980' => 'bca', 'BcaB05g25100' => 'bca', 'BcaB07g32241' => 'bca', 'BcaB07g32242' => 'bca', 'BcaB07g32244' => 'bca', 'BcaB07g32619' => 'bca', 'BcaB08g34239' => 'bca', 'BcaC03g15112' => 'bca', 'BcaC03g15794' => 'bca', 'BcaC03g16835' => 'bca', 'BcaC05g26149' => 'bca', 'BcaC05g26151' => 'bca', 'BcaC05g27045' => 'bca', 'BcaC06g34941' => 'bca', 'BcaC07g38450' => 'bca', 'BcaC07g39148' => 'bca', 'BcaC08g47386' => 'bca', 'BcaC09g51525' => 'bca', 'BcaNung00007' => 'bca', 'BolC1t01202H' => 'bol', 'BolC2t10759H' => 'bol', 'BolC5t30832H' => 'bol', 'BolC5t31634H' => 'bol', 'BolC6t40230H' => 'bol', 'BolC7t42679H' => 'bol', 'BolC7t43478H' => 'bol', 'BolC8t49781H' => 'bol', 'BraA01t00978Z' => 'bra', 'BraA02t07204Z' => 'bra', 'BraA02t07996Z' => 'bra', 'BraA06t27477Z' => 'bra', 'BraA07t29208Z' => 'bra', 'BraA07t31855Z' => 'bra', 'BraA08t34786Z' => 'bra', 'BraA09t39158Z' => 'bra', 'BraA09t39731Z' => 'bra', 'C01p12260' => 'bna', 'C02p35390' => 'bna', 'C02p47130' => 'bna', 'C05p21340' => 'bna', 'C05p29040' => 'bna', 'C06p52070' => 'bna', 'C07p21530' => 'bna', 'C07p29370' => 'bna', 'C08p12190' => 'bna', 'C08p21420' => 'bna', 'CAN.G103.2' => 'can', 'CAN.G1261.6' => 'can', 'CAN.G187.10' => 'can', 'CAN.G379.24' => 'can', 'CAN.G702.35' => 'can', 'CANSAT35G0784' => 'cansat', 'CANSAT35G1025' => 'cansat', 'CARHR022570' => 'chi', 'CARHR029230' => 'chi', 'CARHR071560' => 'chi', 'CARHR175620' => 'chi', 'CARHR225180' => 'chi', 'Carub.0001s2177' => 'cru', 'Carub.0001s2843' => 'cru', 'Carub.0002s2499' => 'cru', 'Carub.0007s2289' => 'cru', 'Carub.0008s0175' => 'cru', 'Ca_00527_v3' => 'car', 'Cc00_g24620' => 'ccan', 'Cc01_g05700' => 'ccan', 'Cc10_g07400' => 'ccan', 'CDE01G0442' => 'cde', 'CDE02G2946' => 'cde', 'CDE04G1188' => 'cde', 'CDE04G1792' => 'cde', 'CDE05G0926' => 'cde', 'CDE05G3417' => 'cde', 'CDE11G0270' => 'cde', 'CDE12G0820' => 'cde', 'Cfa000922' => 'cfa', 'Cfa009836' => 'cfa', 'Cfa013621' => 'cfa', 'Ciclev10001889m.g' => 'ccl', 'Ciclev10015378m.g' => 'ccl', 'Ciclev10015553m.g' => 'ccl', 'CiPaw.07G181400' => 'cil', 'CiPaw.09G121600' => 'cil', 'CiPaw.10G090100' => 'cil', 'CiPaw.13G152500' => 'cil', 'CiPaw.14G115000' => 'cil', 'ClCG01G024750' => 'cla', 'ClCG03G006660' => 'cla', 'ClCG03G012870' => 'cla', 'ClCG08G011030' => 'cla', 'COL.COLO4_07228' => 'col', 'COL.COLO4_16430' => 'col', 'COL.COLO4_31037' => 'col', 'Cpa.g.sc1683.1' => 'cpa', 'Cpa.g.sc36.117' => 'cpa', 'CsaV3_1G004650' => 'csa', 'CsaV3_1G022880' => 'csa', 'CsaV3_1G043180' => 'csa', 'CsaV3_6G051850' => 'csa', 'CSS0005311' => 'camsi', 'CSS0035338' => 'camsi', 'CSS0046911' => 'camsi', 'CSS0050066' => 'camsi', 'DCAR_018591' => 'dca', 'DCAR_027902' => 'dca', 'DCAR_027903' => 'dca', 'Dinv07772' => 'din', 'Dinv07773' => 'din', 'Dinv07778' => 'din', 'Dinv07780' => 'din', 'Dinv07782' => 'din', 'Dinv07792' => 'din', 'Dinv07794' => 'din', 'Dinv07795' => 'din', 'Dinv07797' => 'din', 'Dinv08776' => 'din', 'Dinv12133' => 'din', 'Dinv13029' => 'din', 'Dinv15410' => 'din', 'Dinv32230' => 'din', 'Dinv36165' => 'din', 'Dinv36189' => 'din', 'Dinv42869' => 'din', 'Dinv42870' => 'din', 'Dinv43229' => 'din', 'Dinv43230' => 'din', 'Dinv43231' => 'din', 'Dinv44761' => 'din', 'Duzib116G0234' => 'dzi', 'Duzib160G0608' => 'dzi', 'Duzib168G0794' => 'dzi', 'Duzib168G1589' => 'dzi', 'Duzib170G0084' => 'dzi', 'Duzib192G0528' => 'dzi', 'Duzib235G0395' => 'dzi', 'ECA233G0757' => 'eca', 'ECA233G4194' => 'eca', 'ECA233G5666' => 'eca', 'ECA233G6169' => 'eca', 'ECA234G1213' => 'eca', 'ECA236G1408' => 'eca', 'ECA236G1843' => 'eca', 'ECA238G1040' => 'eca', 'ECA238G2689' => 'eca', 'ECA238G4353' => 'eca', 'ECA240G2306' => 'eca', 'ECA240G4265' => 'eca', 'ECA246G1652' => 'eca', 'ECA247G0263' => 'eca', 'ECA247G3046' => 'eca', 'ECA247G3259' => 'eca', 'ECA247G3492' => 'eca', 'EL10Ac4g10119' => 'bvu', 'EL10Ac4g10169' => 'bvu', 'EL10Ac8g19644' => 'bvu', 'Eucgr.B03721' => 'egr', 'Eucgr.D00284' => 'egr', 'Eucgr.D00286' => 'egr', 'FAN04G0059' => 'fan', 'FAN08G3608' => 'fan', 'FAN11G0544' => 'fan', 'FAN13G3055' => 'fan', 'FAN14G2655' => 'fan', 'FAN14G4139' => 'fan', 'FAN16G2003' => 'fan', 'FAN16G2646' => 'fan', 'FAN18G1587' => 'fan', 'FAN21G0430' => 'fan', 'FAN25G3776' => 'fan', 'FvH4_1g13150' => 'fve', 'FvH4_3g05230' => 'fve', 'FvH4_3g10414' => 'fve', 'FvH4_4g17393' => 'fve', 'FvH4_5g37750' => 'fve', 'Glyma.13G219800' => 'gma', 'Glyma.15G092600' => 'gma', 'Gohir.A05G147400' => 'ghi', 'Gohir.A06G037000' => 'ghi', 'Gohir.A06G138800' => 'ghi', 'Gohir.A06G196600' => 'ghi', 'Gohir.A09G111000' => 'ghi', 'Gohir.A10G042400' => 'ghi', 'Gohir.D05G149900' => 'ghi', 'Gohir.D06G037600' => 'ghi', 'Gohir.D06G143600' => 'ghi', 'Gohir.D06G204100' => 'ghi', 'Gohir.D09G107700' => 'ghi', 'Gohir.D10G043300' => 'ghi', 'Gorai.006G125400' => 'gra', 'Gorai.009G154000' => 'gra', 'Gorai.010G042500' => 'gra', 'Gorai.010G167400' => 'gra', 'Gorai.010G238100' => 'gra', 'Gorai.011G045900' => 'gra', 'GSVIVG01009011001' => 'vvi', 'GSVIVG01021526001' => 'vvi', 'GSVIVG01037246001' => 'vvi', 'GSVIVG01037247001' => 'vvi', 'HanXRQChr02g0032871' => 'han', 'HanXRQChr03g0090081' => 'han', 'HanXRQChr03g0090251' => 'han', 'HanXRQChr03g0090711' => 'han', 'HanXRQChr04g0115701' => 'han', 'HanXRQChr05g0162931' => 'han', 'HanXRQChr11g0327711' => 'han', 'HanXRQChr15g0482061' => 'han', 'HanXRQChr16g0525751' => 'han', 'HanXRQChr17g0542411' => 'han', 'Haze_05628' => 'cav', 'Haze_22247' => 'cav', 'Haze_23203' => 'cav', 'Hma1.2p1_0020F.1_g014200' => 'hma', 'Hma1.2p1_0115F.1_g056030' => 'hma', 'Hma1.2p1_0115F.1_g056035' => 'hma', 'Hma1.2p1_0120F.1_g057280' => 'hma', 'Hma1.2p1_2007F.1_g310920' => 'hma', 'Hma1.2p1_3168F.1_g333540' => 'hma', 'HPP92_000653' => 'vpl', 'HPP92_000693' => 'vpl', 'HPP92_006659' => 'vpl', 'HPP92_012188' => 'vpl', 'HPP92_028711' => 'vpl', 'Lalb_Chr15g0086751' => 'lal', 'Lalb_Chr18g0055311' => 'lal', 'Lalb_Chr20g0117841' => 'lal', 'Lj2P320T24' => 'lonja', 'Lj2P625T49' => 'lonja', 'Lj6g0027783' => 'lja', 'Lju9295C0T5' => 'lonja', 'Lsat_1_v5_gn_2_25220' => 'lsa', 'Lsat_1_v5_gn_3_111980' => 'lsa', 'Lsat_1_v5_gn_3_112301' => 'lsa', 'Lsat_1_v5_gn_3_112361' => 'lsa', 'Lsat_1_v5_gn_3_112381' => 'lsa', 'Lsat_1_v5_gn_3_112420' => 'lsa', 'Lsat_1_v5_gn_3_112461' => 'lsa', 'Lsat_1_v5_gn_3_112541' => 'lsa', 'Lsat_1_v5_gn_3_112621' => 'lsa', 'Lsat_1_v5_gn_3_112881' => 'lsa', 'Lsat_1_v5_gn_3_113520' => 'lsa', 'Lsat_1_v5_gn_3_113540' => 'lsa', 'Lsat_1_v5_gn_3_113660' => 'lsa', 'Lsat_1_v5_gn_3_113880' => 'lsa', 'Lsat_1_v5_gn_3_113900' => 'lsa', 'Lsat_1_v5_gn_3_114020' => 'lsa', 'Lsat_1_v5_gn_4_29661' => 'lsa', 'Lsat_1_v5_gn_5_1361' => 'lsa', 'Lsat_1_v5_gn_5_65001' => 'lsa', 'Lsat_1_v5_gn_6_103700' => 'lsa', 'Lsat_1_v5_gn_7_27760' => 'lsa', 'Manes.02G141400' => 'mes', 'Manes.15G123700' => 'mes', 'Manes.17G072500' => 'mes', 'Mapoly0086s0036' => 'mpo', 'Mapoly0115s0056' => 'mpo', 'Mapoly0142s0022' => 'mpo', 'MBI02_g03071_MAGBIO' => 'mbi', 'MBI02_g42090_MAGBIO' => 'mbi', 'MBI13_g30856_MAGBIO' => 'mbi', 'MBI16_g23778_MAGBIO' => 'mbi', 'MBI19_g28099_MAGBIO' => 'mbi', 'MD05G1281200' => 'mdo', 'MD10G1259600' => 'mdo', 'MD15G1366300' => 'mdo', 'Medtr2g019080' => 'mtr', 'Medtr4g029330' => 'mtr', 'MELO3C002753.2' => 'cme', 'MELO3C007122.2' => 'cme', 'MELO3C011360.2' => 'cme', 'MELO3C015149.2' => 'cme', 'Migut.C00013' => 'egut', 'Migut.D00647' => 'egut', 'Migut.H01354' => 'egut', 'Migut.M00892' => 'egut', 'MSTRG.13256' => 'ama', 'MSTRG.14779' => 'ama', 'MSTRG.16256' => 'ama', 'MSTRG.21355' => 'ama', 'MSTRG.7502' => 'ama', 'Nitab4.5_0000206g0030' => 'nta', 'Nitab4.5_0000675g0050' => 'nta', 'Nitab4.5_0000718g0110' => 'nta', 'Nitab4.5_0001992g0090' => 'nta', 'Nitab4.5_0004020g0020' => 'nta', 'Nitab4.5_0005094g0020' => 'nta', 'Nitab4.5_0006712g0020' => 'nta', 'Nitab4.5_0009172g0030' => 'nta', 'Nn1g05320' => 'nnu', 'Nn1g05632' => 'nnu', 'Nn2g14797' => 'nnu', 'Nn3g18922' => 'nnu', 'Nn3g20411' => 'nnu', 'Nn5g30380' => 'nnu', 'Nn5g30456' => 'nnu', 'Nn6g31510' => 'nnu', 'Nn6g32010' => 'nnu', 'Nn7g36268' => 'nnu', 'Nn7g36743' => 'nnu', 'Nn7g38438' => 'nnu', 'Nn8g38568' => 'nnu', 'Oeu024543.1' => 'oeu', 'Oeu025898.1' => 'oeu', 'Oeu031182.1' => 'oeu', 'Oeu031295.1' => 'oeu', 'Oeu031296.1' => 'oeu', 'Oeu034130.1' => 'oeu', 'Oeu040097.1' => 'oeu', 'Oeu042463.1' => 'oeu', 'Oeu043285.1' => 'oeu', 'Oeu061290.1' => 'oeu', 'Oeu061491.1' => 'oeu', 'Os01g0770400' => 'osa', 'Os01g0812200' => 'osa', 'Os03g0321300' => 'osa', 'Os05g0490300' => 'osa', 'Os05g0510400' => 'osa', 'Peaxi162Scf00041g00091' => 'pax', 'Peaxi162Scf00050g00131' => 'pax', 'Peaxi162Scf00317g00022' => 'pax', 'Peaxi162Scf00465g00113' => 'pax', 'PGR031G1663' => 'pgr', 'PGR042G2047' => 'pgr', 'PGR102G1754' => 'pgr', 'PGSC0003DMG400000773' => 'stu', 'PGSC0003DMG400009478' => 'stu', 'PGSC0003DMG400019053' => 'stu', 'PGSC0003DMG400021165' => 'stu', 'PGSC0003DMG400021302' => 'stu', 'PGSC0003DMG400046726' => 'stu', 'Phvul.006G166500' => 'pvu', 'Potri.002G094600' => 'ptr', 'Potri.004G065900' => 'ptr', 'Potri.005G166500' => 'ptr', 'Potri.009G047600' => 'ptr', 'Potri.011G082900' => 'ptr', 'Pp3c10_10820' => 'ppa', 'Pp3c14_16580' => 'ppa', 'Prupe.1G514000' => 'ppe', 'Prupe.2G108500' => 'ppe', 'Prupe.4G083400' => 'ppe', 'Psat1g188400' => 'psa', 'PSO339G3624' => 'pso', 'PSO384G4114' => 'pso', 'PSO541G2046' => 'pso', 'PSO541G4392' => 'pso', 'PSO675G7017' => 'pso', 'PSO781G0093' => 'pso', 'QL01p017691' => 'qlo', 'QL05p055783' => 'qlo', 'QL05p074450' => 'qlo', 'QL08p013359' => 'qlo', 'QL12p036390' => 'qlo', 'RcHm_v2.0_Chr2g0143491' => 'rch', 'RcHm_v2.0_Chr5g0014481' => 'rch', 'RcHm_v2.0_Chr7g0239491' => 'rch', 'Rhsim04G0137600' => 'rsi', 'Rhsim06G0083900' => 'rsi', 'Rhsim13G0113100' => 'rsi', 'Rhsim13G0115700' => 'rsi', 'Rhsim13G0213300' => 'rsi', 'Rhsim13G0213400' => 'rsi', 'Rhsim13G0213500' => 'rsi', 'Rhsim13G0213600' => 'rsi', 'Rhsim13G0213800' => 'rsi', 'Rhsim13G0213900' => 'rsi', 'Rhsim13G0214000' => 'rsi', 'Rhsim13G0214100' => 'rsi', 'Rhsim13G0214200' => 'rsi', 'Rhsim13G0214400' => 'rsi', 'Rhsim13G0214500' => 'rsi', 'Rhsim13G0214600' => 'rsi', 'Rhsim13G0214700' => 'rsi', 'Rhsim13G0214900' => 'rsi', 'Rhsim13G0215100' => 'rsi', 'Rhsim13G0215200' => 'rsi', 'Rhsim13G0215300' => 'rsi', 'Rhsim13G0215400' => 'rsi', 'Rhsim13G0215600' => 'rsi', 'Rhsim13G0215700' => 'rsi', 'Rhsim13G0215800' => 'rsi', 'Sabra02G0074600' => 'sbr', 'Sabra04G0044000' => 'sbr', 'Sabra05G0125500' => 'sbr', 'Sabra09G0034900' => 'sbr', 'Sabra11G0066000' => 'sbr', 'SalBow6G7265' => 'sbo', 'SalBow7G0637' => 'sbo', 'SalBow8G2781' => 'sbo', 'SalBow8G4972' => 'sbo', 'Sc05g0006060' => 'sci', 'Sc09g0000970' => 'sci', 'Sc17g0004860' => 'sci', 'Sc24g0001690' => 'sci', 'Sc24g0001700' => 'sci', 'Sed0001998' => 'sed', 'Sed0004813' => 'sed', 'Sed0007810' => 'sed', 'Sed0013354' => 'sed', 'Sed0022410' => 'sed', 'Sed0024563' => 'sed', 'SEGI_08982' => 'sgi', 'SEGI_11958' => 'sgi', 'SEGI_18297' => 'sgi', 'SEGI_21453' => 'sgi', 'SEGI_27610' => 'sgi', 'SEGI_34774' => 'sgi', 'SEGI_39800' => 'sgi', 'SGA_v2.0_scaffold1G00196' => 'sas', 'SGA_v2.0_scaffold223G42815' => 'sas', 'SGA_v2.0_scaffold223G42816' => 'sas', 'SGA_v2.0_scaffold29G12211' => 'sas', 'SGA_v2.0_scaffold793G53609' => 'sas', 'SGA_v2.0_scaffold8G04554' => 'sas', 'SHI24848' => 'shi', 'SMO118G0548' => 'smo', 'SMO142G0063' => 'smo', 'SMO205G0014' => 'smo', 'SMO358G0016' => 'smo', 'Solyc02g070480.4' => 'sly', 'Solyc04g072930.1' => 'sly', 'Solyc08g048430.4' => 'sly', 'Sopen02g019570' => 'spe', 'Sopen04g029120' => 'spe', 'Sopen08g010700' => 'spe', 'Sp1g19720' => 'spa', 'Sp1g26020' => 'spa', 'Sp2g11030' => 'spa', 'Sp5g33240' => 'spa', 'Sp7g15660' => 'spa', 'TAR381G0898' => 'tar', 'TAR624G0062' => 'tar', 'TAR625G1176' => 'tar', 'TAR626G1935' => 'tar', 'TAR627G0364' => 'tar', 'TAR629G2565' => 'tar', 'THA.LOC104798397' => 'tha', 'THA.LOC104798398' => 'tha', 'THA.LOC104798466' => 'tha', 'THA.LOC104800155' => 'tha', 'THA.LOC104810852' => 'tha', 'THA.LOC104820656' => 'tha', 'Thecc.06G147600' => 'tca', 'Thecc.08G109300' => 'tca', 'Thecc.09G244200' => 'tca', 'Thhalv10000919m.g' => 'esa', 'Thhalv10007915m.g' => 'esa', 'Thhalv10010014m.g' => 'esa', 'Thhalv10018841m.g' => 'esa', 'Thhalv10025383m.g' => 'esa', 'TPR.G26263' => 'tpr', 'TWI09G1429' => 'twi', 'TWI12G0673' => 'twi', 'TWI36G0747' => 'twi', 'TWI53G0821' => 'twi', 'unitig_26.g9761' => 'ugi', 'unitig_26.g9762' => 'ugi', 'unitig_37.g12094' => 'ugi', 'unitig_749.g13800' => 'ugi', 'unitig_90.g27458' => 'ugi', 'unitig_90.g27459' => 'ugi', 'unitig_92.g28164' => 'ugi', 'VMungo0540G0846' => 'vmu', 'VMungo1215G2208' => 'vmu', 'Zm00001eb106070' => 'zma', 'Zm00001eb139210' => 'zma', 'Zm00001eb149190' => 'zma', 'Zm00001eb150090' => 'zma', 'Zm00001eb152000' => 'zma', 'Zm00001eb291260' => 'zma', 'Zm00001eb292460' => 'zma', 'Zm00001eb352260' => 'zma', 'Zm00001eb352820' => 'zma' ) $gf_id = 'HOM05D001192' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001192' ) $data_identifier = 'HOM05D001192' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 20, 'aar' => (int) 5, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 21, 'bol' => (int) 8, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 22, 'dzi' => (int) 7, 'eca' => (int) 17, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 11, 'fve' => (int) 5, 'gma' => (int) 2, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 5, 'lal' => (int) 3, 'lonja' => (int) 3, 'lja' => (int) 1, 'lsa' => (int) 21, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 5, 'mdo' => (int) 3, 'mtr' => (int) 2, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 13, 'oeu' => (int) 11, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 1, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 1, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 25, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 7, 'vmu' => (int) 2, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb352820' $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